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The easiest way to insert new rows of EMS code in a program object is using a text editor (NotePad, e.g.). Below is an example of inserting three new EMS lines in a program after line A4.

EnergyManagementSystem:Program,
  VAV_5_NightCycleMGR,     !- Name
  SET Toffset = 0.8333,    !- Program Line 1
  SET NoAction = 0.0,      !- Program Line 2
  SET ForceOff = 1.0,      !- A4
  New EMS Line 1,
  New EMS Line 2,
  New EMS Line 3,
  SET CycleOn = 2.0,       !- A5
  ...

Notice that I have not added comments after !- to the right of each new EMS line. After saving the IDF in your text editor, you can then open the same updated IDF in IDF Editor. If you save in IDF editor, it will automatically update the line number comments to the right for you (see below).

EnergyManagementSystem:Program,
  VAV_5_NightCycleMGR,     !- Name
  SET Toffset = 0.8333,    !- Program Line 1
  SET NoAction = 0.0,      !- Program Line 2
  SET ForceOff = 1.0,      !- A4
  New EMS Line 1,          !- A5
  New EMS Line 2,          !- A6
  New EMS Line 3,          !- A7
  SET CycleOn = 2.0,       !- A8
  ...